Merge pull request #2 from Tuks-ICMM/PCA-and-Fixation

Pca and fixation

config/config.json

@@ -13,49 +13,10 @@
             ]
         }
     ],
-    "environment": {
-        "email": {
-            "address": "[email protected]",
-            "conditions": [
-                "o",
-                "e"
-            ]
-        },
-        "queues": [
-            {
-                "queue": "normal",
-                "walltime": "30:00:00",
-                "memory": "128G",
-                "cores": "10",
-                "nodes": "1",
-                "rules": [
-                    "Admixture_v1p3",
-                    "Plink_PCA",
-                    "PLINK",
-                    "DAPC"
-                ]
-            },
-            {
-                "queue": "short",
-                "walltime": "00:30:00",
-                "memory": "128G",
-                "cores": "14",
-                "nodes": "1",
-                "rules": [
-                    "plinkPed",
-                    "fetchPedLables",
-                    "Admixture_v1p3_Graphs",
-                    "Plink2_Graphs"
-                ]
-            }
-        ],
-        "envmodules": {
-            "plink-2": "plink-2",
-            "plink-1.9": "plink-1.9",
-            "structure": "structure-2.3.4",
-            "admixture-1.3": "admixture-1.3.0",
-            "r": "R-4.1.3",
-            "python-3": "python-3.11.3"
-        }
-    }
+    "output-dir": [
+        "/",
+        "mnt",
+        "ICMM_HDD_12TB",
+        "Results_25SEP2024"
+    ]
 }

docs/02-workflow/02-analysis.md

@@ -26,4 +26,37 @@ Reference Genome Configuration
 {:toc}
 </details>
 
----
+---
+
+<details>
+  <summary>Rule Map/Diagram</summary>
+
+  ```mermaid
+    flowchart TB
+      classDef bcftools stroke:#FF5733,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef plink stroke:#36454F,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef python stroke:#FEBE10,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef admixture stroke:#333,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef tabix stroke:#023020,fill:#D3D3D3,stroke-width:4px,color:black;
+      classDef gatk stroke:#007FFF,fill:#D3D3D3,stroke-width:4px,color:black;
+      START(((Input)))
+      END(((Output)))
+
+      extract_provided_region[[**extract_provided_region**: Extract the provided region coordinates for clustering]]
+
+      remove_rare_variants[[**remove_rare_variants**: Remove all variants which are not good indicators of population structure by nature]]
+
+      plinkPca[[**Plink_PCA**:
+  Perform a PLINK-2.0 PCA]]
+      
+      report_fixation_index_per_cluster[[**report_fixation_index_per_cluster**: Report Fixation-index for the provided clusters]]
+
+      class remove_rare_variants,plinkPca,plinkPed,report_fixation_index_per_cluster,extract_provided_region plink;
+      class Admixture admixture;
+      class fetchPedLables python;
+
+      START --> extract_provided_region --> remove_rare_variants --> plinkPca & report_fixation_index_per_cluster
+
+      plinkPca & report_fixation_index_per_cluster --> END
+  ```
+</details>